A new computing architecture that mimics the behavior of biological cells (called a whole cell computer) is defined by this patent application. The Whole Cell Computer (WCC) is a computational architecture only (and is therefore independent of what hardware or physical implementation is used to render it) and it is based on the biochemical processing of cells, it “computes” by cooperating with a “network” of WCCs, and it is “programmed” by genetic recombinations. It draws from recent success in molecular biology, bioinformatics and systems biology and it offers the promise of a machine that can solve pattern recognition problems, complex simulation problems and biochemical process problems (such as drug delivery or toxicity assessment). Depending upon the physical implementation, a WCC could also have significant relevance to the field of nanotechnology.